BS1002 Biophysical Chemistry SPARTAN 1

BS1002 Biophysical Chemistry
Introduction to computational chemistry calculations of electronic structure and bonding
Chong Jia Yun

Using a computer software called Spartan, users can build molecules and derive useful data such as the structure and bonding energy of the interested molecule within a short span of time.

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The practical aims to depict bonding concepts and orbitals of molecules through the computation of organic compounds using Spartan. This is achieved by building molecules, performing calculations and analysing results.

During this lab session, acrylonitrile, cyclohexanone, oxygen and carbon monoxide molecules were built and analysed. Measurements of acrylonitrile and cyclohexanone were made with Equilibrium Geometry calculation using basis set 3-21G*. Measurements of oxygen and carbon monoxide molecules were made with Density Functional calculation using basis set 6-31G* except for finding energy using Energy calculation with basis set 6-31G*.

Calculation records to be accounted for in report:
All bond distances, total energy, dipole moment and two selected bond angles of acrylonitrile.

Total energy, dipole moment and a figure of the LUMO orbital of cyclohexanone.

Total energies of all states of oxygen molecule.

Total energies and bonding energy calculation of carbon monoxide and oxygen molecules.

Exercise 1: Computation for acrylonitrile

Figure SEQ Figure * ARABIC 1: Acrylonitrile (ball-and-spoke model)
Bond distances in the molecule
Bond Bond distance
C3 – C2 1.427 Å
C2 = C1 1.319 Å
N1 ? C3 1.140 Å
C1 – H2, C1 – H3, C2 – H4 1.072 Å
Bond distance
Bond distance is the internuclear distance between two atoms that are covalently bonded. It is dependent on the size of atoms that are bonded and the bond order.
From the above results, C3 – C2 has a greater bond distance than the bond distance between a carbon atom and a hydrogen atom even though they all have single bonds. This is because the smaller the size of the atoms, the shorter the bond distance. Since a H atom is smaller than a C atom, a H atom can be more closely bonded to a C atom as compared to two carbon atoms, thus shorter bond distance between hydrogen and carbon.

The above results also reflect the effect of bond order on bond distance. The bond distance increases as such: N1 ? C3 < C2 = C1 < C3 – C2. This is because the higher the bond order between any 2 atoms, the greater the degree of orbital overlap, the stronger the bond, the shorter the bond distance.
Bond Bond order
C3 – C2 1
C2 = C1 2
N1 ? C3 3
In this case, N1 ? C3 has the highest bond order, thus it has the shortest bond distance.

Total energy and dipole moment
Total energy: -168.820401 hartreesDipole moment: 4.03 debyeDipole moment
When atoms of 2 different elements form a covalent bond, the bonding electrons are not equally shared between the atoms due to each atom having a different electronegativity.

The more electronegative atom will attract the bonding electrons more strongly. This will result in the more electronegative atom acquiring a partial negative charge and the other atom acquiring a partial positive charge.

This separation of charge results in a dipole and the formation of a polar covalent bond.
Value of two selected bond angles (between three connected atoms)
Bond Bond angle
C3 – C2 – H4 115.69°
N1 – C3 – C2 179.89°
Bond angle

Exercise 2: Computation for cyclohexanone

Figure SEQ Figure * ARABIC 2: Cyclohexanone (ball-and-spoke model)
Total energy and dipole moment
Total energy: – hartreesDipole moment: debyeLUMO orbital

Figure SEQ Figure * ARABIC 3: LUMO orbital

Figure SEQ Figure * ARABIC 4: LUMO orbital

Figure SEQ Figure * ARABIC 5: LUMO map
Comment on the result with respect to reactivity

Exercise 3: Determine the ground state of O2 molecule

Figure SEQ Figure * ARABIC 6: O2 molecule (ball-and-spoke model)
Total energy of all states
Total energy of oxygen molecule (unpaired): -150.267048 hartreesTotal energy of oxygen molecule (paired): -150.204729 hartreesGround state of oxygen
Compare the HOMO and LUMO orbitals

Figure SEQ Figure * ARABIC 7: aLUMO
Figure SEQ Figure * ARABIC 8: bLUMO
Figure SEQ Figure * ARABIC 9: aHOMO
Figure SEQ Figure * ARABIC 10: bHOMODiscussion

Exercise 4: Which molecule CO or O2 is more stable

Figure SEQ Figure * ARABIC 11: Carbon monoxide (ball-and-spoke model)
Energy of CO: -113.270306 hartreesEnergy of O2: -150.267048 hartreesEnergy of C: -37.830235 hartreesEnergy of O: -75.036232 hartreesBonding energy of CO
= -113.270306 – -37.830235 + (-75.036232)
= -0.403839 hartreesBonding energy of O2
= -150.267048 – -75.036232 + (-75.036232)
= -0.194584 hartreesDiscussion